FMO DATABASE

FMODB ID: 52KYZ

Calculation Name: 3BJA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BJA

Chain ID: A

ChEMBL ID:

UniProt ID: Q738D3

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1205278.096041
FMO2-HF: Nuclear repulsion	1146880.791674
FMO2-HF: Total energy	-58397.304368
FMO2-MP2: Total energy	-58561.848187

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-8.711	-6.613	7.286	-4.437	-4.947	-0.01

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.008

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	2	ASN	0	0.080	0.036	2.556	-4.359	-1.906	0.671	-1.497	-1.628	-0.014
4	A	3	ASN	0	0.006	0.001	2.178	-3.767	-4.410	6.615	-2.853	-3.118	0.004
5	A	4	ARG	1	0.944	0.971	4.034	-0.029	0.259	0.000	-0.087	-0.201	0.000
6	A	5	GLU	-1	-0.895	-0.960	6.118	-0.486	-0.486	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.014	0.029	7.269	0.202	0.202	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.025	-0.019	8.174	0.088	0.088	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.023	-0.002	10.048	0.001	0.001	0.000	0.000	0.000	0.000
10	A	9	ASN	0	0.031	0.008	11.665	0.050	0.050	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.008	0.009	12.496	0.022	0.022	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.878	0.933	14.135	-0.203	-0.203	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.867	-0.925	16.035	-0.051	-0.051	0.000	0.000	0.000	0.000
14	A	13	VAL	0	0.007	-0.001	17.641	0.004	0.004	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.023	-0.006	18.960	0.009	0.009	0.000	0.000	0.000	0.000
16	A	15	HIS	0	0.017	-0.012	18.787	0.002	0.002	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.047	-0.023	21.506	0.000	0.000	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.034	0.023	22.670	0.001	0.001	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.024	-0.007	24.666	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.952	0.980	26.464	0.023	0.023	0.000	0.000	0.000	0.000
21	A	20	ASN	0	-0.019	-0.030	28.040	0.002	0.002	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.026	0.012	29.523	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.792	-0.917	30.777	0.026	0.026	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.774	0.881	32.618	0.005	0.005	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.004	0.004	33.989	0.000	0.000	0.000	0.000	0.000	0.000
26	A	25	ILE	0	-0.064	-0.037	34.511	0.000	0.000	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.831	-0.890	37.270	0.001	0.001	0.000	0.000	0.000	0.000
28	A	27	GLN	0	-0.008	-0.013	38.610	0.000	0.000	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.063	-0.035	40.471	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.944	-0.959	41.398	0.014	0.014	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.112	-0.059	38.075	0.004	0.004	0.000	0.000	0.000	0.000
32	A	31	SER	0	0.027	0.006	33.391	0.000	0.000	0.000	0.000	0.000	0.000
33	A	32	TYR	0	0.020	-0.019	27.763	0.002	0.002	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.028	-0.009	31.439	0.002	0.002	0.000	0.000	0.000	0.000
35	A	34	GLN	0	0.051	0.014	32.710	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.049	0.033	33.117	0.000	0.000	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.031	0.012	32.748	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	37	VAL	0	0.012	-0.006	33.592	0.000	0.000	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.008	0.003	36.362	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.008	-0.009	34.898	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	40	VAL	0	-0.020	-0.017	33.599	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.045	-0.044	36.393	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	42	ALA	0	0.012	0.026	39.808	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.773	0.903	34.950	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.017	0.007	39.001	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.058	0.025	40.797	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.825	0.896	43.108	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.019	0.026	39.283	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	SER	0	0.041	0.026	40.752	0.000	0.000	0.000	0.000	0.000	0.000
50	A	49	MET	0	0.012	-0.015	38.476	0.000	0.000	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.005	0.013	36.792	0.002	0.002	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.906	0.934	34.700	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.012	0.004	35.483	0.001	0.001	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.028	-0.034	32.112	0.002	0.002	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.869	-0.927	31.301	0.073	0.073	0.000	0.000	0.000	0.000
56	A	55	ASN	0	-0.024	-0.016	30.531	0.006	0.006	0.000	0.000	0.000	0.000
57	A	56	MET	0	-0.054	-0.004	30.800	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.005	0.007	27.072	0.006	0.006	0.000	0.000	0.000	0.000
59	A	58	CYS	0	-0.027	-0.016	24.549	0.016	0.016	0.000	0.000	0.000	0.000
60	A	59	VAL	0	0.022	0.020	26.524	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	60	PRO	0	-0.001	0.004	28.185	0.007	0.007	0.000	0.000	0.000	0.000
62	A	61	SER	0	0.021	0.002	29.362	0.000	0.000	0.000	0.000	0.000	0.000
63	A	62	ASN	0	0.006	-0.012	31.129	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	63	MET	0	0.088	0.056	33.391	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	64	THR	0	0.030	0.012	35.904	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	65	THR	0	0.001	0.003	38.471	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	66	MET	0	-0.037	0.000	34.780	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	67	ILE	0	0.060	0.009	37.810	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	68	GLN	0	0.027	0.007	40.781	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	69	ARG	1	0.893	0.965	41.167	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	70	MET	0	0.076	0.032	39.383	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.889	0.962	43.150	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.755	0.861	44.904	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.791	-0.874	44.108	0.022	0.022	0.000	0.000	0.000	0.000
75	A	74	GLY	0	0.017	0.029	47.061	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.010	0.018	43.315	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.019	0.000	41.851	0.000	0.000	0.000	0.000	0.000	0.000
78	A	77	MET	0	-0.007	0.005	45.292	0.000	0.000	0.000	0.000	0.000	0.000
79	A	78	THR	0	-0.020	-0.033	44.434	0.001	0.001	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.797	-0.866	47.309	0.025	0.025	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.881	0.955	46.382	-0.039	-0.039	0.000	0.000	0.000	0.000
82	A	81	ASN	0	-0.001	-0.015	47.183	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	82	PRO	0	0.001	-0.009	50.012	0.001	0.001	0.000	0.000	0.000	0.000
84	A	83	ASN	0	-0.031	0.010	50.550	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	84	ASP	-1	-0.779	-0.863	47.291	0.044	0.044	0.000	0.000	0.000	0.000
86	A	85	GLN	0	0.105	0.029	48.922	0.001	0.001	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.789	0.869	46.059	-0.044	-0.044	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.865	-0.927	43.356	0.047	0.047	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.070	-0.041	43.816	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	89	LEU	0	0.019	0.017	43.712	0.003	0.003	0.000	0.000	0.000	0.000
91	A	90	VAL	0	-0.010	-0.030	41.598	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	91	TYR	0	-0.025	-0.033	43.901	0.000	0.000	0.000	0.000	0.000	0.000
93	A	92	LEU	0	0.037	0.032	41.993	0.000	0.000	0.000	0.000	0.000	0.000
94	A	93	THR	0	-0.032	-0.018	45.501	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.982	0.982	48.104	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.954	0.979	47.063	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.028	0.025	45.139	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.911	-0.951	44.371	0.018	0.018	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.964	-1.004	45.874	0.009	0.009	0.000	0.000	0.000	0.000
100	A	99	THR	0	0.010	-0.021	42.398	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.806	0.904	39.380	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.861	0.934	41.873	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.004	-0.003	43.857	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	103	VAL	0	0.037	0.029	38.003	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	104	ASP	-1	-0.799	-0.896	38.788	0.010	0.010	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.016	0.001	39.180	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	106	GLN	0	0.100	0.050	38.117	0.000	0.000	0.000	0.000	0.000	0.000
108	A	107	TYR	0	-0.012	-0.001	30.652	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	108	SER	0	-0.009	-0.009	34.578	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.837	-0.921	35.684	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	110	PHE	0	0.015	0.014	28.027	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	111	LEU	0	0.010	-0.003	29.912	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.821	0.916	30.878	0.012	0.012	0.000	0.000	0.000	0.000
114	A	113	GLU	-1	-0.949	-0.976	32.129	-0.026	-0.026	0.000	0.000	0.000	0.000
115	A	114	ASN	0	-0.078	-0.039	27.943	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	115	CYS	0	-0.080	-0.036	26.833	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.037	0.023	27.849	0.000	0.000	0.000	0.000	0.000	0.000
118	A	117	CYS	0	-0.061	-0.025	25.243	0.000	0.000	0.000	0.000	0.000	0.000
119	A	118	PHE	0	-0.026	0.002	21.496	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	119	THR	0	0.010	-0.027	26.811	0.009	0.009	0.000	0.000	0.000	0.000
121	A	120	LYS	1	0.811	0.859	27.832	0.044	0.044	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.942	-0.961	26.460	-0.096	-0.096	0.000	0.000	0.000	0.000
123	A	122	GLU	-1	-0.813	-0.887	23.536	-0.119	-0.119	0.000	0.000	0.000	0.000
124	A	123	GLU	-1	-0.828	-0.893	23.389	-0.052	-0.052	0.000	0.000	0.000	0.000
125	A	124	GLY	0	0.051	0.032	24.551	0.005	0.005	0.000	0.000	0.000	0.000
126	A	125	ILE	0	0.000	0.006	19.922	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	126	LEU	0	-0.015	-0.018	18.667	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-0.948	-0.971	20.090	-0.019	-0.019	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.873	-0.938	20.863	-0.052	-0.052	0.000	0.000	0.000	0.000
130	A	129	LEU	0	-0.085	-0.044	15.273	0.007	0.007	0.000	0.000	0.000	0.000
131	A	130	LEU	0	-0.002	-0.008	16.589	0.022	0.022	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.013	-0.012	18.244	0.033	0.033	0.000	0.000	0.000	0.000
133	A	132	LYS	1	0.929	0.971	14.515	0.141	0.141	0.000	0.000	0.000	0.000
134	A	133	TRP	0	-0.007	-0.008	10.856	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	134	LYS	1	0.950	0.968	15.452	0.000	0.000	0.000	0.000	0.000	0.000
136	A	135	LYS	1	0.936	0.964	18.500	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	136	HIS	0	-0.028	0.007	11.417	-0.050	-0.050	0.000	0.000	0.000	0.000
138	A	137	LEU	0	-0.024	-0.013	12.715	0.041	0.041	0.000	0.000	0.000	0.000
139	A	138	ASN	0	-0.046	-0.003	16.136	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)